Offboarding after Save

src/petab_gui/controllers/mother_controller.py

@@ -42,6 +42,7 @@
     process_file,
 )
 from ..views import TaskBar
+from ..views.other_views import NextStepsPanel
 from .logger_controller import LoggerController
 from .sbml_controller import SbmlController
 from .table_controllers import (
@@ -150,6 +151,11 @@ def __init__(self, view, model: PEtabModel):
         }
         self.sbml_checkbox_states = {"sbml": False, "antimony": False}
         self.unsaved_changes = False
+        # Next Steps Panel
+        self.next_steps_panel = NextStepsPanel(self.view)
+        self.next_steps_panel.dont_show_again_changed.connect(
+            self._handle_next_steps_dont_show_again
+        )
         self.filter = QLineEdit()
         self.filter_active = {}  # Saves which tables the filter applies to
         self.actions = self.setup_actions()
@@ -489,6 +495,12 @@ def setup_actions(self):
             )
         )
 
+        # Show next steps panel action
+        actions["next_steps"] = QAction(
+            qta.icon("mdi6.lightbulb-on"), "Possible next steps...", self.view
+        )
+        actions["next_steps"].triggered.connect(self._show_next_steps_panel)
+
         # Undo / Redo
         actions["undo"] = QAction(qta.icon("mdi6.undo"), "&Undo", self.view)
         actions["undo"].setShortcut(QKeySequence.Undo)
@@ -582,6 +594,13 @@ def save_model(self):
             "Save Project",
             f"Project saved successfully to {file_name}",
         )
+
+        # Show next steps panel if not disabled
+        if not settings_manager.get_value(
+            "next_steps/dont_show_again", False, bool
+        ):
+            self.next_steps_panel.show_panel()
+
         return True
 
     def save_single_table(self):
@@ -1414,6 +1433,14 @@ def about(self):
             f"<a href='file://{config_file}'>{config_file}</a></small>",
         )
 
+    def _show_next_steps_panel(self):
+        """Show the next steps panel (ignores 'don't show again' preference)."""
+        self.next_steps_panel.show_panel()
+
+    def _handle_next_steps_dont_show_again(self, dont_show: bool):
+        """Handle the 'don't show again' checkbox in the next steps panel."""
+        settings_manager.set_value("next_steps/dont_show_again", dont_show)
+
     def get_current_problem(self):
         """Get the current PEtab problem from the model."""
         return self.model.current_petab_problem

src/petab_gui/views/other_views.py

@@ -1,13 +1,18 @@
 """Collection of other views aside from the main ones."""
 
+from PySide6.QtCore import Qt, Signal
 from PySide6.QtWidgets import (
+    QCheckBox,
     QComboBox,
     QDialog,
+    QFrame,
     QHBoxLayout,
     QLabel,
     QLineEdit,
     QPushButton,
+    QTextBrowser,
     QVBoxLayout,
+    QWidget,
 )
 
 
@@ -64,3 +69,211 @@ def get_result(self) -> tuple[str | None, str | None]:
         time_text = (self._time.text() or "").strip() or None
         preeq = (self._preeq_edit.text() or "").strip()
         return dose, time_text, preeq
+
+
+class NextStepsPanel(QWidget):
+    """Non-modal panel showing possible next steps after saving."""
+
+    dont_show_again_changed = Signal(bool)
+
+    def __init__(self, parent=None):
+        super().__init__(parent, Qt.Window | Qt.WindowStaysOnTopHint)
+        self.setWindowTitle("Possible next steps")
+        self.setMinimumWidth(450)
+        self.setMaximumWidth(600)
+        self.setMinimumHeight(360)
+
+        # Main layout
+        main_layout = QVBoxLayout(self)
+        main_layout.setContentsMargins(12, 12, 12, 12)
+        main_layout.setSpacing(10)
+
+        # Description
+        desc = QLabel(
+            "This parameter estimation problem can now be used in the following tools:"
+        )
+        desc.setWordWrap(True)
+        main_layout.addWidget(desc)
+
+        # Main suggestions
+        suggestions_layout = QVBoxLayout()
+        suggestions_layout.setSpacing(8)
+
+        # pyPESTO action
+        pypesto_frame = QFrame()
+        pypesto_frame.setStyleSheet(
+            "QFrame { background-color: rgba(100, 149, 237, 0.08); "
+            "border-radius: 4px; padding: 8px; }"
+        )
+        pypesto_layout = QVBoxLayout(pypesto_frame)
+        pypesto_layout.setContentsMargins(8, 8, 8, 8)
+        pypesto_layout.setSpacing(4)
+
+        pypesto_text = QTextBrowser()
+        pypesto_text.setOpenExternalLinks(True)
+        pypesto_text.setFrameStyle(QFrame.NoFrame)
+        pypesto_text.setStyleSheet("QTextBrowser { background: transparent; }")
+        pypesto_text.setVerticalScrollBarPolicy(
+            Qt.ScrollBarPolicy.ScrollBarAlwaysOff
+        )
+        pypesto_text.setHtml(
+            '<p style="margin:0; line-height:1.3;">'
+            "<b>▶ Parameter estimation</b><br/>"
+            "Use pyPESTO for parameter estimation and uncertainty "
+            "analysis<br/>"
+            '<a href="https://pypesto.readthedocs.io/en/latest/example/'
+            'petab_import.html">pyPESTO documentation</a></p>'
+        )
+        pypesto_layout.addWidget(pypesto_text)
+        suggestions_layout.addWidget(pypesto_frame)
+
+        # COPASI action
+        copasi_frame = QFrame()
+        copasi_frame.setStyleSheet(
+            "QFrame { background-color: rgba(169, 169, 169, 0.08); "
+            "border-radius: 4px; padding: 8px; }"
+        )
+        copasi_layout = QVBoxLayout(copasi_frame)
+        copasi_layout.setContentsMargins(8, 8, 8, 8)
+        copasi_layout.setSpacing(4)
+
+        copasi_text = QTextBrowser()
+        copasi_text.setOpenExternalLinks(True)
+        copasi_text.setFrameStyle(QFrame.NoFrame)
+        copasi_text.setStyleSheet("QTextBrowser { background: transparent; }")
+        copasi_text.setVerticalScrollBarPolicy(
+            Qt.ScrollBarPolicy.ScrollBarAlwaysOff
+        )
+        copasi_text.setHtml(
+            '<p style="margin:0; line-height:1.3;">'
+            "<b>⚙ Model adjustment and simulation</b><br/>"
+            "Use COPASI for further model adjustment and advanced "
+            "simulation<br/>"
+            '<a href="https://copasi.org">COPASI website</a></p>'
+        )
+        copasi_layout.addWidget(copasi_text)
+        suggestions_layout.addWidget(copasi_frame)
+
+        main_layout.addLayout(suggestions_layout)
+
+        # Collapsible section for other tools
+        self._other_tools_btn = QPushButton(
+            "📊 ▶ Other tools supporting PEtab"
+        )
+        self._other_tools_btn.setCheckable(True)
+        self._other_tools_btn.setFlat(True)
+        self._other_tools_btn.setStyleSheet(
+            "QPushButton { text-align: left; padding: 6px; "
+            "font-weight: normal; }"
+            "QPushButton:checked { font-weight: bold; }"
+        )
+        self._other_tools_btn.clicked.connect(self._toggle_other_tools)
+        main_layout.addWidget(self._other_tools_btn)
+
+        # Other tools frame (initially hidden)
+        self._other_tools_frame = QFrame()
+        self._other_tools_frame.setStyleSheet(
+            "QFrame { background-color: rgba(144, 238, 144, 0.08); "
+            "border-radius: 4px; padding: 8px; }"
+        )
+        self._other_tools_frame.setVisible(False)
+        other_tools_layout = QVBoxLayout(self._other_tools_frame)
+        other_tools_layout.setContentsMargins(8, 8, 8, 8)
+        other_tools_layout.setSpacing(4)
+
+        # Framing text
+        framing_text = QLabel("Additional tools in the PEtab ecosystem:")
+        framing_text.setWordWrap(True)
+        other_tools_layout.addWidget(framing_text)
+
+        other_tools_text = QTextBrowser()
+        other_tools_text.setOpenExternalLinks(True)
+        other_tools_text.setMaximumHeight(120)
+        other_tools_text.setFrameStyle(QFrame.NoFrame)
+        other_tools_text.setStyleSheet(
+            "QTextBrowser { background: transparent; }"
+        )
+        other_tools_text.setVerticalScrollBarPolicy(
+            Qt.ScrollBarPolicy.ScrollBarAsNeeded
+        )
+        other_tools_text.setHtml(
+            '<ul style="margin:4px 0; padding-left: 20px; '
+            'line-height: 1.6;">'
+            '<li style="margin-bottom: 4px;">'
+            '<a href="https://amici.readthedocs.io/en/latest/examples/'
+            'example_petab/petab.html">AMICI</a> - '
+            "Advanced simulation and sensitivity analysis</li>"
+            '<li style="margin-bottom: 4px;">'
+            '<a href="https://github.com/Data2Dynamics/d2d/wiki">'
+            "Data2Dynamics</a> - "
+            "Comprehensive modeling environment</li>"
+            '<li style="margin-bottom: 4px;">'
+            '<a href="https://parpe.readthedocs.io">parPE</a> - '
+            "Parallel parameter estimation</li>"
+            '<li style="margin-bottom: 4px;">'
+            '<a href="https://petab.readthedocs.io/en/latest/v1/'
+            'software_support.html">PEtab documentation</a> - '
+            "Full list of supporting tools</li>"
+            "</ul>"
+        )
+        other_tools_layout.addWidget(other_tools_text)
+
+        main_layout.addWidget(self._other_tools_frame)
+
+        # Spacer
+        main_layout.addStretch()
+
+        # Reassurance text
+        reassurance = QLabel(
+            "<small><i>You can always access this dialog from the "
+            "Help menu.</i></small>"
+        )
+        reassurance.setWordWrap(True)
+        reassurance.setStyleSheet("QLabel { color: gray; padding: 0; }")
+        main_layout.addWidget(reassurance)
+
+        # Bottom section with checkbox and close button
+        bottom_layout = QHBoxLayout()
+        bottom_layout.setSpacing(8)
+
+        self._dont_show_checkbox = QCheckBox("Don't show after saving")
+        self._dont_show_checkbox.stateChanged.connect(
+            lambda state: self.dont_show_again_changed.emit(
+                state == Qt.CheckState.Checked
+            )
+        )
+        bottom_layout.addWidget(self._dont_show_checkbox)
+
+        bottom_layout.addStretch()
+
+        close_btn = QPushButton("Close")
+        close_btn.clicked.connect(self.close)
+        close_btn.setDefault(True)
+        bottom_layout.addWidget(close_btn)
+
+        main_layout.addLayout(bottom_layout)
+
+    def _toggle_other_tools(self, checked):
+        """Toggle visibility of other tools section."""
+        self._other_tools_frame.setVisible(checked)
+        # Update button text to show expand/collapse state
+        arrow = "▼" if checked else "▶"
+        icon = "📊"
+        self._other_tools_btn.setText(
+            f"{icon} {arrow} Other tools supporting PEtab"
+        )
+        # Adjust window size
+        self.adjustSize()
+
+    def show_panel(self):
+        """Show the panel and center it on the parent."""
+        if self.parent():
+            # Center on parent window
+            parent_geo = self.parent().geometry()
+            self.move(
+                parent_geo.center().x() - self.width() // 2,
+                parent_geo.center().y() - self.height() // 2,
+            )
+        self.show()
+        self.raise_()
+        self.activateWindow()

src/petab_gui/views/task_bar.py

@@ -136,6 +136,8 @@ def __init__(self, parent, actions):
 
         # Add actions to the menu for re-adding tables
         self.menu.addAction(actions["open_documentation"])
+        self.menu.addAction(actions["next_steps"])
+        self.menu.addSeparator()
         self.menu.addAction(actions["whats_this"])
         self.menu.addAction(actions["about"])